Moved identity check functions from script into module
Added --plink and --manifest arguments to check_identity_bed.pl and moved QC test data into pipeline test directory
Working first draft of flexible identity threshold
Major refactoring to implement flexible identity threshold and improved swap check
Remove --manifest argument and add --swap
Removed --manifest argument
Changed identity input file
Write dummy JSON output if insufficient SNPs found
Read identity results from JSON file
Change identity input filename
Deleted obsolete test input
initial commit
Changed arguments to check_identity script
updated manifest for new identity test data
Added no-warning option
Change arguments to check_identity_bed.pl; check for id_json output; supply id_json to createReports
Supply identity JSON to createReports
Single method to write JSON output, with additional information
update for new identity JSON format
updated identity_check JSON format